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Jchem bases: the problem of standardier molecular structure
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Xiaoya

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Link to postPosted: Sat Aug 30, 2014 1:32 pmPost subject: Jchem bases: the problem of standardier molecular structure Reply with quote

Dear engineer,
   (1) Which action can I choose to build my configuration as shown at the step 2 "configure actions"?(aromatize,clean2D,or...)
   (2) How can I operate to import a configuration at the second step ?
   When press the button of "import", I need to input a standardizer configuration file. But it is terrible that I can`t find the .xml file in my computer then how can I do to solve this problem?
   (3) How can I set the chosen actions` parameters? For example, which scheme options can I choose for the action of "Transform Nitro" ?
   It is my honor to get your reply.
                                                                               Sincerely,Xiaoya Song.
Xiaoya

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Link to postPosted: Sat Aug 30, 2014 2:32 pmPost subject: Reply with quote

If I input ( .cdx) file, for example ethanol's .cdx file, How can I operate at the second step in Standardizer software to get the .sdf output file.

Krisztina
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Link to postPosted: Mon Sep 01, 2014 12:28 pmPost subject: Reply with quote

Hi Xiaoya,

Your questions are answered here.

Best regards

Krisztina

Xiaoya

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Link to postPosted: Tue Sep 09, 2014 9:43 amPost subject: standaradizer structual Reply with quote

kvajda wrote:

Hi Xiaoya,

Your questions are answered here.

Best regards

Krisztina

Dear professor Krisztina,

   Thank you for your guidance. That's very nice of you.

   I have studied the website that you give , however still don't know which configure action is need to standaradizer molecular structure as the following format:

   Could you help me?

   Best wishes to you.

                                                                                                           Sincerely, Xiaoya Song.




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Zsolt
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Link to postPosted: Wed Sep 10, 2014 8:06 amPost subject: Reply with quote

I guess you want to add explicit hydrogens to the molecule (with the Add Explicit Hydrogens action), and use SDF output format.

Xiaoya

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Link to postPosted: Wed Sep 10, 2014 2:08 pmPost subject: Reply with quote

Zsolt wrote:

I guess you want to add explicit hydrogens to the molecule (with the Add Explicit Hydrogens action), and use SDF output format.

Dear professor Zsolt,

     When I chose the Add Explicit Hydrogens action, the SDF output format see figure1. 

    When I chose the "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action +"Map"action+"Clean 2D"action , the SDF output format see figure 2. It is the same result with [ "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action+"Clean 2D"action ]

 

    However, these (figure1/figure2) aren't the result that I want to get.

   So, I want to know how to change my configuration to get the result of the "structural information" figure.





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Xiaoya

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Link to postPosted: Wed Sep 10, 2014 2:09 pmPost subject: Reply with quote

missducksong wrote:
Zsolt wrote:

I guess you want to add explicit hydrogens to the molecule (with the Add Explicit Hydrogens action), and use SDF output format.

Dear professor Zsolt,

     When I chose the Add Explicit Hydrogens action, the SDF output format see figure1. 

    When I chose the "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action +"Map"action+"Clean 2D"action , the SDF output format see figure 2. It is the same result with [ "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action+"Clean 2D"action ]

 

    However, these (figure1/figure2) aren't the result that I want to get.

   So, I want to know how to change my configuration to get the result of the "structural information" figure.





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Xiaoya

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Link to postPosted: Wed Sep 10, 2014 2:10 pmPost subject: Reply with quote

missducksong wrote:
missducksong wrote:
Zsolt wrote:

I guess you want to add explicit hydrogens to the molecule (with the Add Explicit Hydrogens action), and use SDF output format.

Dear professor Zsolt,

     When I chose the Add Explicit Hydrogens action, the SDF output format see figure1. 

    When I chose the "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action +"Map"action+"Clean 2D"action , the SDF output format see figure 2. It is the same result with [ "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action+"Clean 2D"action ]

 

    However, these (figure1/figure2) aren't the result that I want to get.

   So, I want to know how to change my configuration to get the result of the "structural information" figure.





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structural information.jpg
Zsolt
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Link to postPosted: Fri Sep 12, 2014 10:07 amPost subject: Reply with quote

Please explain in plain English what do you want to do with your chemical structure (in this case it is ethanol, so the possibilities are quite limited).

Xiaoya

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Link to postPosted: Fri Sep 12, 2014 4:40 pmPost subject: Reply with quote

Zsolt wrote:

Please explain in plain English what do you want to do with your chemical structure (in this case it is ethanol, so the possibilities are quite limited).

Dear Professer,

   I want to calculate fragments simplex descriptors values with my chemical structure, as shown in Figure1.




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Zsolt
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Link to postPosted: Tue Sep 16, 2014 2:24 pmPost subject: Reply with quote

So your workflow is:

input molecule  --(Standardizer)-->  standardized molecule  --(descriptor calculator)-->  descriptors

Your descriptor calculator expects the molecules to be in a certain state (e.g. 2D/3D coordinates, explicit hydrogens, aromatized) and format (e.g. SDF). Let us know the expected state and format and we can help.

Xiaoya

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Link to postPosted: Wed Sep 17, 2014 9:37 amPost subject: Reply with quote

Zsolt wrote:

So your workflow is:

input molecule  --(Standardizer)-->  standardized molecule  --(descriptor calculator)-->  descriptors

Your descriptor calculator expects the molecules to be in a certain state (e.g. 2D/3D coordinates, explicit hydrogens, aromatized) and format (e.g. SDF). Let us know the expected state and format and we can help.

Dear professor,

   Thank you for your help. It is my honor to get your guidance.

   My workflow is just as you say, input molecule --(Standardizer)--> standardized molecule --(descriptor calculator)-->  descriptors. And I indeed need the molecules to be in a certain state. 

  In terms of the molecule structure, my expected state and format is like the examples as shown in figures.That is, I want to get ethanol/n-butanol/i-propanol/acetone/butanone-2/cyclopentanone's style as shown in Figure 1/2/3/4/5/6 respectively at the same time.

Figure1

Figure2

Figure3

Figure4

Figure5

Figure6

Your help is highly appreciated, and I look forward to hearing from you.

Xiaoya

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Link to postPosted: Tue Sep 23, 2014 7:51 amPost subject: Reply with quote

Zsolt wrote:

So your workflow is:

input molecule  --(Standardizer)-->  standardized molecule  --(descriptor calculator)-->  descriptors

Your descriptor calculator expects the molecules to be in a certain state (e.g. 2D/3D coordinates, explicit hydrogens, aromatized) and format (e.g. SDF). Let us know the expected state and format and we can help.

Dear professor,

     How can I solve the above problems?

    Hope your solutions and help.

Zsolt
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Link to postPosted: Fri Sep 26, 2014 11:45 amPost subject: Reply with quote

The information you provided is not enough to suggest a proper solution. I can see on SDfile screenshots (these are text files, why don't you attach them?) that the molecules contain explicit hydrogens, and they have 2D coordinates. Based on that I can recommend this standardizer configuration:

Add Explicit Hydrogens
Clean 2D

Xiaoya

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Link to postPosted: Wed Oct 08, 2014 4:11 pmPost subject: standardizer problem Reply with quote

Zsolt wrote:

The information you provided is not enough to suggest a proper solution. I can see on SDfile screenshots (these are text files, why don't you attach them?) that the molecules contain explicit hydrogens, and they have 2D coordinates. Based on that I can recommend this standardizer configuration:

Add Explicit Hydrogens
Clean 2D

Dear engineers,

        I am very interested in molecular structure standardizer. I think it is important and  meaningful. Recently, I reinstall my work computer (win7 32bit) at the same time to reinstall this calculation software. 

       However, when I use ethanol's .cdx file as input file (C2H6O.cdx) and select “Add Explicit HydrogensClean 2D” as this standardizer configuration, both the standardizer structures and the SDF output file are 0 as shown in Figure 1.

      No matter how can I adjust the configuration [for example, chose the "Add Explicit Hydrogens "action +"Alias to Atom" action+ "Alias to Group" action+"Dearomatize" action +"Map"action+"Clean 2D"action], the output file is always empty. What's going wrong?

      Your help is highly appreciated, and I look forward to hearing from you!

      Best regards.

   

   




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Zsolt
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Link to postPosted: Thu Oct 09, 2014 8:37 amPost subject: Reply with quote

Please attach the input file (C2H6O.cdx).

Xiaoya

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Link to postPosted: Fri Oct 10, 2014 8:00 amPost subject: Reply with quote

Zsolt wrote:

Please attach the input file (C2H6O.cdx).




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Xiaoya

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Link to postPosted: Tue Oct 21, 2014 6:17 amPost subject: Re: standardizer problem Reply with quote

missducksong wrote:
Zsolt wrote:

The information you provided is not enough to suggest a proper solution. I can see on SDfile screenshots (these are text files, why don't you attach them?) that the molecules contain explicit hydrogens, and they have 2D coordinates. Based on that I can recommend this standardizer configuration:

Add Explicit Hydrogens
Clean 2D

Dear engineer,

        Recently I have solved the question of output file empty.

      At the same time, I have used the method that you give ("Add Explicit Hydrogens"+"Clean 2D") to standardizer the structure of ethanol. Unfortunately, the result is not the value of my except, as shown in figure1. While my except the ethanol's value as shown in figure2.

       Dear engineer, How can I do to make a apposite  configure to  calculate my except result like figure 2 ?

      Thank you for your help, it is significant to me.

      Best regards.

                                                                                           Sincerely, Xiaoya song.

   

   




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Zsolt
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Link to postPosted: Wed Oct 29, 2014 5:01 pmPost subject: Reply with quote

We discovered a bug: standardizer generated 3D coordinates for the molecule in C2H6O.cdx file with configuration "Add Explicit Hydrogens"+"Clean 2D". We have fixed the bug, the fixed version will be available next week.

Output with the fixed version:

  Mrv0541 10291417012D          

  9  8  0  0  0  0            999 V2000
    1.7495   -1.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3370   -1.2190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5120   -1.2190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0350   -2.3460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1620   -2.6480    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4640   -1.5210    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0263   -0.7657    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3850   -0.3954    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0995   -0.5046    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  9  1  0  0  0  0
M  END
$$$$

Is this what you expect?

Xiaoya

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Link to postPosted: Thu Dec 25, 2014 6:34 amPost subject: Reply with quote

Dear engineer,

         Thank you for your help. It can correctly calculate now.

         Best wish to you !

                                                               (*^__^*) 

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